seekia/resources/geneticReferences/traits/traits.go

// traits provides information about traits and the SNPs that influence them

package traits

// TODO: We want to eventually use neural nets for both trait and polygenic disease analysis
// These will be trained on a set of genomes and will output a probability analysis for each trait
// This is only possible once we get access to the necessary training data
//
// See geneticPrediction.go for a non-working attempt to predict traits with neural nets

import "errors"

type RuleLocus struct{

	// 3 byte hex encoded string
	LocusIdentifier string

	// RSID that represents this locus
	// If multiple RSIDs represent the same locus, use the first rsid for the locus in the locusMetadata package
	LocusRSID int64

	// List of base pair values that this RSID must fulfill to pass the rule
	// As long as the value matches any base pair value in the list, the genome has passed this rule locus
	// The genome must pass every rule locus within a rule to pass the rule
	BasePairsList []string
}


type TraitRule struct{

	// 3 byte identifier encoded hex
	RuleIdentifier string 

	// A list of RuleLocus objects which comprise the rule
	// The genome must have a required base pair for each locus in this list to pass the rule
	LociList []RuleLocus

	// The outcome that this rule will effect
	// The number of points to add to the outcome if the rule RSID values are fulfilled
	// Do not use negative values

	// Map Structure: Outcome name -> Points to add to outcome if rule passes
	OutcomePointsMap map[string]int

	// Map structure: Reference name -> Reference link
	References map[string]string
}


type Trait struct{

	TraitName string

	TraitDescription string

	// This is a list of rsIDs which are known to have an effect on this trait
	// These loci may not have any associated rules
	// We use these loci to calculate Racial Similarity.
	// We will also use neural networks to predict trait outcome scores using these loci
	LociList []int64

	// This list can be empty if no rules exist
	// An empty list means we are relying on LociList and neural networks for trait prediction.
	RulesList []TraitRule

	// List of outcomes
	// Example: "Lactose Intolerant", "Lactore Tolerant"
	// This list can be empty if outcomes are not text descriptions (Example: Facial structure)
	// If there are no outcomes, then no rules can exist
	OutcomesList []string

	// Map structure: Reference name -> Reference link
	References map[string]string
}

var traitNamesList []string
var traitObjectsList []Trait

// Map Structure: Rule locus identifier -> RSID representing this locus 
var locusRSIDsMap map[string]int64

func InitializeTraitVariables(){

	lactoseToleranceObject := getLactoseToleranceTraitObject()
	hairTextureObject := getHairTextureTraitObject()
	facialStructureObject := getFacialStructureTraitObject()
	eyeColorObject := getEyeColorTraitObject()
	hairColorObject := getHairColorTraitObject()
	skinColorObject := getSkinColorTraitObject()

	traitObjectsList = []Trait{lactoseToleranceObject, hairTextureObject, facialStructureObject, eyeColorObject, hairColorObject, skinColorObject}

	traitNamesList = make([]string, 0, len(traitObjectsList))
	locusRSIDsMap = make(map[string]int64)

	for _, traitObject := range traitObjectsList{

		traitName := traitObject.TraitName

		traitNamesList = append(traitNamesList, traitName)

		traitRulesList := traitObject.RulesList

		for _, traitRuleObject := range traitRulesList{

			ruleLociList := traitRuleObject.LociList

			for _, ruleLocusObject := range ruleLociList{

				locusIdentifier := ruleLocusObject.LocusIdentifier
				locusRSID := ruleLocusObject.LocusRSID

				locusRSIDsMap[locusIdentifier] = locusRSID
			}
		}
	}
}

// Be aware that all of these functions are returning original objects/slices, not copies
// Thus, we cannot edit the objects/slices that are returned. We must copy the fields first if we want to edit them.

func GetTraitNamesList()([]string, error){

	if (traitNamesList == nil){
		return nil, errors.New("GetTraitNamesList called when list is not initialized.")
	}
	
	return traitNamesList, nil
}

func GetTraitObjectsList()([]Trait, error){

	if (traitObjectsList == nil){
		return nil, errors.New("GetTraitObjectsList called when list is not initialized.")
	}

	return traitObjectsList, nil
}

func GetTraitObject(traitName string)(Trait, error){

	traitObjectsList, err := GetTraitObjectsList()
	if (err != nil) { return Trait{}, err }

	for _, traitObject := range traitObjectsList{

		currentTraitName := traitObject.TraitName
		if (currentTraitName != traitName){
			continue
		}

		return traitObject, nil
	}

	return Trait{}, errors.New("GetTraitObject called with unknown trait: " + traitName)
}

//Outputs:
//	-map[string]TraitRule: Map of RuleIdentifier -> Rule Object
//	-error (will return err if traitName is not found)
func GetTraitRulesMap(traitName string)(map[string]TraitRule, error){

	traitObject, err := GetTraitObject(traitName)
	if (err != nil) { return nil, err }

	traitRulesList := traitObject.RulesList

	traitRulesMap := make(map[string]TraitRule)

	for _, ruleObject := range traitRulesList{

		ruleIdentifier := ruleObject.RuleIdentifier
		traitRulesMap[ruleIdentifier] = ruleObject
	}

	return traitRulesMap, nil
}

func GetTraitRuleObject(traitName string, ruleIdentifier string)(TraitRule, error){

	traitRulesMap, err := GetTraitRulesMap(traitName)
	if (err != nil){ return TraitRule{}, err }

	ruleObject, exists := traitRulesMap[ruleIdentifier]
	if (exists == false){
		return TraitRule{}, errors.New("GetTraitRuleObject called with unknown ruleIdentifier: " + ruleIdentifier)
	}

	return ruleObject, nil
}

//Outputs:
//	-int64: The rsID which represents this locus
//	-error
func GetTraitRuleLocusRSID(locusIdentifier string)(int64, error){

	if (locusRSIDsMap == nil){
		return 0, errors.New("GetTraitRuleLocusRSID called when locusRSIDsMap is not initialized.")
	}

	locusRSID, exists := locusRSIDsMap[locusIdentifier]
	if (exists == false){
		return 0, errors.New("GetTraitRuleLocusRSID called with unknown locusIdentifier: " + locusIdentifier)
	}

	return locusRSID, nil
}